10-88660884-G-C

Position:

• chr10-88660884-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.555 in 151,830 control chromosomes in the GnomAD database, including 24,014 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.56 (24014 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.444

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.869 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.88660884G>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84224 AN: 151712 Hom.: 23973 Cov.: 31

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.587

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.555 AC: 84320 AN: 151830 Hom.: 24014 Cov.: 31 AF XY: 0.562 AC XY: 41660 AN XY: 74184

Gnomad4 AFR AF: 0.608

Gnomad4 AMR AF: 0.606

Gnomad4 ASJ AF: 0.594

Gnomad4 EAS AF: 0.890

Gnomad4 SAS AF: 0.661

Gnomad4 FIN AF: 0.485

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.591

Alfa AF: 0.359 Hom.: 969

Bravo AF: 0.567

Asia WGS AF: 0.794 AC: 2760 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.52

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1214451; hg19: chr10-90420641;